As a result of studies conducted by the human genome project, base sequences of the full set of genes, “a draft of the human life”, will be elucidated within a few years. It is known that diseases or senescence will be developed if the draft has a defect or is injured. As the results of development of the human genome project, many diseases including cancer can be elucidated in a DNA level, and the total medical sciences consisting mainly of diagnosis and prevention are believed to be changed revolutionarily. Further, although we have a great expectation for developments of a therapeutic method based on understanding in DNA levels of diseases and pharmaceuticals targeting in causal genes of the diseases or their products, studies of such fundamental researches mediating to clinical studies have just started. Antitumor drugs used at present are mainly antibiotics selected by screening works, and originally are not the product produced by microorganisms for the purpose of killing tumor cells. Furthermore few drug based on the molecular biological knowledge on tumor has been known. If an expression of an intracellular specific gene can be freely controlled extracellularly, an ultimate therapeutic method in a gene level can be achieved.
We, recently, found that an antibiotic duocarmycin could construct a heterodimer with other kinds of molecules such as distamycin to perform cooperatively molecular recognition of DNA and also perform efficiently an alkylation to a base sequence different from the case of duocarmycin alone (Proc. Natl. Acad. Sci. USA 93, 14405, 1996). Based on the results of this study, we succeeded to synthesize a molecule which could selectively alkylate DNA at any position of its base sequence, by binding pyrrole-imidazole polyamide as a recognition site for DNA to the active alkylation site of duocarmycin, and applied a patent (JP-A-10-260710).
However, the compounds, in which the pyrrole-imidazole polyamide as a DNA recognition site is bound only in the active alkylation site of duocarmycin, are not only insufficient in the alkylation activity but also able only to recognize a single-stranded base sequence. Consequently, we examined alkylation mechanisms between these molecules and DNA in detail using a computer modeling such as molecular dynamics of these compounds, and found that double-stranded DNA could be simultaneously alkylated and cleaved by introducing a linker such as vinyl group into the cyclopropane moiety (segment A), an active site of duocarmycin (JP-A-11-83591).
From the fact that these artificial chemical species, which could recognize base sequences of natural DNA and RNA, recognized a specific base sequence of the natural DNA and RNA, and affected an action of the segment A to the specific site of the DNA and RNA, we found that these artificial chemical species could be applied in place of a partial sequence of the natural DNA and RNA.